[ome-users] bio-formats Micromanager reader issue
Melissa Linkert
melissa at glencoesoftware.com
Sun Jun 3 01:09:04 BST 2012
Hi Colin,
> When attempting to read a micromanager file using the bio-formats ImageJ
> plugin (v. 4.3.3 as well as the latest trunk build, running latest Fiji on
> ubuntu 12.04), I've encountered an exception with the stack trace included
> below. I think this results from micromanager having created a metadata
> field with a value of only empty square brackets in the metadata.txt file.
> I've attached a sample metadata.txt file (one of the empty fields is
> "CustomIntervals_ms": [] at line 47, e.g.); I'm happy to ftp the actual
> images to you as well, though they are too large to attach.
*snip*
> Caused by: java.lang.StringIndexOutOfBoundsException: String index out of
> range: -1
> at java.lang.String.substring(String.java:1937)
> at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:285)
> at loci.formats.FormatReader.setId(FormatReader.java:1072)
> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:481)
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
> at loci.plugins.in.Importer.showDialogs(Importer.java:125)
> at loci.plugins.in.Importer.run(Importer.java:77)
> at loci.plugins.LociImporter.run(LociImporter.java:79)
> at ij.IJ.runUserPlugIn(IJ.java:185)
> at ij.IJ.runPlugIn(IJ.java:152)
> ... 8 more
Thank you for the bug report.
I wasn't able to duplicate this error message using the very latest
trunk build, or the latest version that is in the Fiji updater (and in
fact, I do recall fixing this very bug a while back).
Could you please run the Fiji updater ("Help > Update Fiji", making sure
to update "plugins/loci_tools.jar"), restart Fiji, and then see if the
file opens correctly?
Regards,
-Melissa
On Fri, Jun 01, 2012 at 03:37:54PM -0700, Colin Fuller wrote:
> Hi--
>
> When attempting to read a micromanager file using the bio-formats ImageJ
> plugin (v. 4.3.3 as well as the latest trunk build, running latest Fiji on
> ubuntu 12.04), I've encountered an exception with the stack trace included
> below. I think this results from micromanager having created a metadata
> field with a value of only empty square brackets in the metadata.txt file.
> I've attached a sample metadata.txt file (one of the empty fields is
> "CustomIntervals_ms": [] at line 47, e.g.); I'm happy to ftp the actual
> images to you as well, though they are too large to attach.
>
> Thanks,
>
> Colin Fuller
>
> Stack trace:
>
> java.lang.reflect.InvocationTargetException
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at ij.Command.runPlugIn(Command.java:146)
> at ij.Command.runCommand(Command.java:95)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:680)
> Caused by: java.lang.StringIndexOutOfBoundsException: String index out of
> range: -1
> at java.lang.String.substring(String.java:1937)
> at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:285)
> at loci.formats.FormatReader.setId(FormatReader.java:1072)
> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:481)
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
> at loci.plugins.in.Importer.showDialogs(Importer.java:125)
> at loci.plugins.in.Importer.run(Importer.java:77)
> at loci.plugins.LociImporter.run(LociImporter.java:79)
> at ij.IJ.runUserPlugIn(IJ.java:185)
> at ij.IJ.runPlugIn(IJ.java:152)
> ... 8 more
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> "CoolsnapHQ-Trigger Timeout (secs)": "2",
> "ZStage-Description": "ASI Z-stage driver adapter",
> "ElapsedTime-ms": 1213,
> "Wheel-A-Name": "Wheel-A",
> "Wheel-B-Speed": "3",
> "CoolsnapHQ-TransposeXY": "0",
> "CoolsnapHQ-Firmware Version": "2132",
> "Wheel-A-Description": "Sutter Lambda filter wheel adapter",
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> "CoolsnapHQ-ClearMode": "Clear Pre-Exposure",
> "CoolsnapHQ-TriggerMode": "Timed",
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> "CoolsnapHQ-ChipName": "ICX285 ",
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> "CoolsnapHQ-ReadoutRate": "10MHz 12bit",
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> "CoolsnapHQ-TransposeCorrection": "0",
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> "Wheel-A-ClosedPosition": "",
> "CoolsnapHQ-Gain": "2",
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> "CoolsnapHQ-Description": "PVCAM API device adapter",
> "ZStage-Axis": "Z",
> "COM7-Description": "Serial port driver (boost:asio)",
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> "CoolsnapHQ-Offset": "2593",
> "Wheel-A-Busy": "0",
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> "Core-XYStage": "",
> "Wheel-B-Label": "Filter-4",
> "AxisPositions": null,
> "COM8-Parity": "None",
> "CoolsnapHQ-PMode": "Normal Parallel Clocking",
> "Time": "2012-06-01 10:14:46 -0700",
> "CoolsnapHQ-Binning": "1",
> "Epi-Port": "COM7",
> "COM7-Verbose": "1",
> "CoolsnapHQ-PVCAM Version": "2.7.6",
> "Epi-Name": "Shutter-A 10-2",
> "Wheel-B-Busy": "0",
> "Core-AutoFocus": "",
> "COM7-StopBits": "1",
> "CoolsnapHQ-ActualInterval-ms": "0.0000",
> "Wheel-B-Name": "Wheel-B",
> "COM8-DelayBetweenCharsMs": "0.0000",
> "BitDepth": 12,
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> "CoolsnapHQ-CCDTemperatureSetPoint": "-30",
> "Wheel-A-Label": "Filter-5",
> "COM8-AnswerTimeout": "500.0000",
> "Wheel-B-Description": "Sutter Lambda filter wheel adapter",
> "CoolsnapHQ-Exposure": "2000.00",
> "ChannelIndex": 2,
> "Wheel-B-Port": "COM7",
> "Core-Shutter": "Epi",
> "COM7-BaudRate": "9600",
> "Wheel-A-State": "5",
> "UUID": "7cf28ff0-9a64-4fd3-b9c1-407cb02760c5",
> "Epi-Description": "Sutter Lambda shutter adapter",
> "Core-Camera": "CoolsnapHQ",
> "CoolsnapHQ-PostscanPixels": "40",
> "Core-TimeoutMs": "5000",
> "Core-SLM": "",
> "CoolsnapHQ-Trigger Timeout (secs)": "2",
> "ZStage-Description": "ASI Z-stage driver adapter",
> "ElapsedTime-ms": 6390,
> "Wheel-A-Name": "Wheel-A",
> "Wheel-B-Speed": "3",
> "CoolsnapHQ-TransposeXY": "0",
> "CoolsnapHQ-Firmware Version": "2132",
> "Wheel-A-Description": "Sutter Lambda filter wheel adapter",
> "Frame": 0,
> "Wheel-A-Port": "COM7",
> "Core-ChannelGroup": "Channel",
> "PositionIndex": 0,
> "Width": 1392,
> "WaitInterval": null,
> "PositionName": null,
> "PixelSizeUm": 0,
> "Height": 1040,
> "Summary": {
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> "Interval_ms": 0,
> "UUID": "775aaa0b-87c9-4142-9586-d508da358802",
> "UserName": "cfuller",
> "Depth": 2,
> "PixelType": "GRAY16",
> "Time": "2012-06-01 10:14:40 -0700",
> "Date": "2012-06-01",
> "z-step_um": 0.25,
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> "PositionIndex": 0,
> "SlicesFirst": false,
> "ChContrastMin": [
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> "Width": 1392,
> "PixelAspect": 1,
> "MicroManagerVersion": "1.4.10",
> "ROI": [
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> 0,
> 1392,
> 1040
> ],
> "ChNames": [
> "DAPI",
> "FITC",
> "RHOD"
> ],
> "IJType": 1,
> "GridRow": 0,
> "Comment": "",
> "Height": 1040,
> "GridColumn": 0,
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